Experimental and pan-cancer genome analyses reveal widespread contribution of acrylamide exposure to carcinogenesis in humans

Human cancer genomes harbor the mutational signature of tobacco-specific nitrosamines NNN and NNK

Tobacco usage is linked to multiple cancer types and accounts for a quarter of all cancer-related deaths. Tobacco smoke contains various carcinogenic compounds, including polycyclic aromatic hydrocarbons (PAH), though the mutagenic potential of many tobacco-related chemicals remains largely unexplored. In particular, the highly carcinogenic tobacco-specific nitrosamines NNN and NNK form pre-mutagenic pyridyloxobutyl (POB) DNA adducts. In the study presented here, we identified genome-scale POB-induced mutational signatures in cell lines and rat tumors, while also investigating their role in human cancer. These signatures are characterized by T>N and C>T mutations forming from specific POB adducts damaging dT and dC residues. Analysis of 2,780 cancer genomes uncovered POB signatures in ∼180 tumors; from cancer types distinct from the ones linked to smoking-related signatures SBS4 and SBS92. This suggests that, unlike PAH compounds, the POB pathway may contribute uniquely to the mutational landscapes of certain hematological malignancies and cancers of the kidney, breast, prostate and pancreas.

Acrylamide in food products and the role of electrochemical biosensors in its detection: a comprehensive review

In this review, the mechanisms of acrylamide formation in food, along with aspects related to its toxicity and associated consumption risks, are investigated, highlighting the potential impact on human health. European regulations regarding acrylamide content in food products are also addressed, emphasizing the importance of monitoring and detecting this substance in nutrition, by public health protection measures. The primary objective of the research is to explore and analyze innovative methods for detecting acrylamide in food, with a particular focus on electrochemical biosensors. This research direction is motivated by the need to develop rapid, sensitive, and efficient monitoring techniques for this toxic compound in food products, considering the associated consumption risks. The research has revealed several significant results. Studies have shown that electrochemical biosensors based on hemoglobin exhibited increased sensitivity and low detection limits, capable of detecting very low concentrations of acrylamide in processed foods. Additionally, it has been found that the use of functionalized nanomaterials, such as carbon nanotubes and gold nanoparticles, has led to the improvement of electrochemical biosensor performance in acrylamide detection. The integration of these technological innovations and functionalization strategies has enhanced the sensitivity, specificity, and stability of biosensors in measuring acrylamides. Thus, the results of this research offer promising perspectives for the development of precise and efficient methods for monitoring acrylamides in food, contributing to the improvement of food quality control and the protection of consumer health.

Acceleration of hydrolytic ring opening of N7-alkylguanine by the terminal carbamoyl group of glycidamide

Hydrolytic ring opening of guanine N7-adducts with compounds containing an oxacyclopropane ring, namely glycidamide, glycidol and 1,2-epoxybutane, was analyzed, and the reaction of the glycidamide adduct was the fastest. The differences in the reaction rates were confirmed by theoretical calculations.

Toxicity, metabolism, and mitigation strategies of acrylamide: a comprehensive review

Acrylamide, a food-borne chemical toxicant, has raised global concern in recent decades. It mainly originated from reducing sugar and free amino acid interactions in the carbohydrate-rich foodstuffs heated at high temperatures. Due to the neurotoxicity and carcinogenicity of AA, the mechanism of formation, toxic effects on health, and mitigation strategies, including conventional approaches and innovative technologies, have been of great interest since its discovery in food. Potato products (especially French fries and crisps), coffee, and cereals(bread and biscuit) are renowned contributors to AA's daily intake. The best preventive methods discussed in the literature include time/temperature optimization, blanching, enzymatic treatment, yeast treatment, additives, pulsed electric fields, ultrasound, vacuum roasting, air frying, and irradiation, exhibiting a high efficacy in AA elimination in food products.

Molecular landscapes of oral cancers of unknown etiology

The incidence of the mobile tongue cancer in young patients has been rising. This oral cancer (OC) type has no identified risk factors (NIRF), no established molecular markers and is not yet recognized as a distinct clinical entity. To understand this emerging malignancy, we innovatively analyzed the public head and neck cancer multi-omics data. We identified mutational signatures that successfully stratified 307 OC and 109 laryngeal cancer cases according to their clinico-pathological characteristics. The NIRF OCs exhibited significantly increased activities of endogenous clock-like and APOBEC-associated mutagenesis, alongside specific cancer driver gene mutations, distinct methylome patterns and prominent antimicrobial transcriptomic responses. Furthermore, we show that mutational signature SBS16 in OCs reflects the combined effects of alcohol drinking and tobacco smoking. Our study characterizes the unique disease histories and molecular programs of the NIRF OCs revealing that this emerging cancer subtype is likely driven by increased endogenous mutagenesis correlated with responses to microbial insults.

Two decades of research in dietary acrylamide: What do we know today

After nearly two decades since acrylamide was first raised as a potential safety issue in foods, significant progress has been made in understanding its formation during cooking, how to reduce levels in the most concerned foods, and the possible cancer risk to humans. Despite the huge wealth of knowledge gathered on this topic over the past years, a few new discoveries in occurrence, mitigation, analysis and risk assessment are worthy to note. This short review highlights the salient novelties pertaining to acrylamide, particularly in the areas of formation & analysis, existing and possible future regulations in the European Union, and finally considerations that may lead to possibly revisiting the toxicity of acrylamide and the main metabolite, glycidamide.

Glycidamide-induced hypermutation in yeast single-stranded DNA reveals a ubiquitous clock-like mutational motif in humans

Mutagens often prefer specific nucleotides or oligonucleotide motifs that can be revealed by studying the hypermutation spectra in single-stranded (ss) DNA. We utilized a yeast model to explore mutagenesis by glycidamide, a simple epoxide formed endogenously in humans from the environmental toxicant acrylamide. Glycidamide caused ssDNA hypermutation in yeast predominantly in cytosines and adenines. The most frequent mutations in adenines occurred in the nAt→nGt trinucleotide motif. Base substitutions A→G in this motif relied on Rev1 translesion polymerase activity. Inactivating Rev1 did not alter the nAt trinucleotide preference, suggesting it may be an intrinsic specificity of the chemical reaction between glycidamide and adenine in the ssDNA. We found this mutational motif enriched in published sequencing data from glycidamide-treated mouse cells and ubiquitous in human cancers. In cancers, this motif was positively correlated with the single base substitution (SBS) smoking-associated SBS4 signature, with the clock-like signatures SBS1, SBS5, and was strongly correlated with smoking history and with age of tumor donors. Clock-like feature of the motif was also revealed in cells of human skin and brain. Given its pervasiveness, we propose that this mutational motif reflects mutagenic lesions to adenines in ssDNA from a potentially broad range of endogenous and exogenous agents.

Reducing the Risk of Acrylamide and Other Processing Contaminant Formation in Wheat Products

Wheat is a staple crop, consumed worldwide as a major source of starch and protein. Global intake of wheat has increased in recent years, and overall, wheat is considered to be a healthy food, particularly when products are made from whole grains. However, wheat is almost invariably processed before it is consumed, usually via baking and/or toasting, and this can lead to the formation of toxic processing contaminants, including acrylamide, 5-hydroxymethylfurfural (HMF) and polycyclic aromatic hydrocarbons (PAHs). Acrylamide is principally formed from free (soluble, non-protein) asparagine and reducing sugars (glucose, fructose and maltose) within the Maillard reaction and is classified as a Group 2A carcinogen (probably carcinogenic to humans). It also has neurotoxic and developmental effects at high doses. HMF is also generated within the Maillard reaction but can also be formed via the dehydration of fructose or caramelisation. It is frequently found in bread, biscuits, cookies, and cakes. Its molecular structure points to genotoxicity and carcinogenic risks. PAHs are a large class of chemical compounds, many of which are genotoxic, mutagenic, teratogenic and carcinogenic. They are mostly formed during frying, baking and grilling due to incomplete combustion of organic matter. Production of these processing contaminants can be reduced with changes in recipe and processing parameters, along with effective quality control measures. However, in the case of acrylamide and HMF, their formation is also highly dependent on the concentrations of precursors in the grain. Here, we review the synthesis of these contaminants, factors impacting their production and the mitigation measures that can be taken to reduce their formation in wheat products, focusing on the role of genetics and agronomy. We also review the risk management measures adopted by food safety authorities around the world.

Topography of mutational signatures in human cancer

The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay between mutational signatures and topographical genomic features has not been extensively explored. Here, we integrate mutations from 5,120 whole-genome-sequenced tumors from 40 cancer types with 516 topographical features from ENCODE to evaluate the effect of nucleosome occupancy, histone modifications, CTCF binding, replication timing, and transcription/replication strand asymmetries on the cancer-specific accumulation of mutations from distinct mutagenic processes. Most mutational signatures are affected by topographical features, with signatures of related etiologies being similarly affected. Certain signatures exhibit periodic behaviors or cancer-type-specific enrichments/depletions near topographical features, revealing further information about the processes that imprinted them. Our findings, disseminated via the COSMIC (Catalog of Somatic Mutations in Cancer) signatures database, provide a comprehensive online resource for exploring the interactions between mutational signatures and topographical features across human cancer.

A formamidopyrimidine derivative from the deoxyguanosine adduct produced by food contaminant acrylamide induces DNA replication block and mutagenesis

Acrylamide, a common food contaminant, is metabolically activated to glycidamide, which reacts with DNA at the N7 position of dG, forming N7-(2-carbamoyl-2-hydroxyethyl)-dG (GA7dG). Owing to its chemical lability, the mutagenic potency of GA7dG has not yet been clarified. We found that GA7dG undergoes ring-opening hydrolysis to form N6-(2-deoxy-d-erythro-pentofuranosyl)-2,6-diamino-3,4-dihydro-4-oxo-5-[N-(2-carbamoyl-2-hydroxyethyl)formamido]pyrimidine (GA-FAPy-dG), even at neutral pH. Therefore, we aimed to examine the effects of GA-FAPy-dG on the efficiency and fidelity of DNA replication using an oligonucleotide carrying GA-FAPy-9-(2-deoxy-2-fluoro-β-d-arabinofuranosyl)guanine (dfG), a 2'-fluorine substituted analog of GA-FAPy-dG. GA-FAPy-dfG inhibited primer extension by both human replicative DNA polymerase ε and the translesion DNA synthesis polymerases (Polη, Polι, Polκ, and Polζ) and reduced the replication efficiency by less than half in human cells, with single base substitution at the site of GA-FAPy-dfG. Unlike other formamidopyrimidine derivatives, the most abundant mutation was G:C > A:T transition, which was decreased in Polκ- or REV1-KO cells. Molecular modeling suggested that a 2-carbamoyl-2-hydroxyethyl group at the N5 position of GA-FAPy-dfG can form an additional H-bond with thymidine, thereby contributing to the mutation. Collectively, our results provide further insight into the mechanisms underlying the mutagenic effects of acrylamide.

A rational approach for 3D recognition and removal of L-asparagine via molecularly imprinted membranes

In this study, a L-asparagine (L-Asn) imprinted membranes (L-Asn-MIPs) were synthesized via molecular imprinting for selective and efficient removal of L-Asn. The L-Asn-MIP membrane was prepared by using acrylamide (AAm) and hydroxyethyl methacrylate (HEMA) as a functional monomer and a comonomer, respectively. The membrane was characterized by scanning electron microscopy (SEM) and Fourier Transform infrared spectroscopy (FTIR). The L-Asn adsorption capacity of the membrane was investigated in detail. The maximum L-Asn adsorption capacity was determined as 408.2 mg/g at pH: 7.2, 24 °C. Determination of L-Asn binding behaviors of L-Asn-MIPs also shown with Scatchard analyses. The effect of pH on L-Asn adsorption onto the membrane and also the selectivity and reusability of the L-Asn-MIPs for L-Asn adsorption were determined through L-asparaginase (L-ASNase) enzyme activity measurements. The selectivity of the membrane was investigated by using two different ternary mixtures; L-glycine (L-Gly)/L-histidine (L-His)/L-Asn and L-tyrosin (L-Tyr)/L-cystein(L-Cys)/L-Asn. The obtained results showed that the L-Asn-MIP membranes have a high selectivity towards L-Asn.

DNA damage and somatic mutations in mammalian cells after irradiation with a nail polish dryer

Ultraviolet A light is commonly emitted by UV-nail polish dryers with recent reports suggesting that long-term use may increase the risk for developing skin cancer. However, no experimental evaluation has been conducted to reveal the effect of radiation emitted by UV-nail polish dryers on mammalian cells. Here, we show that irradiation by a UV-nail polish dryer causes high levels of reactive oxygen species, consistent with 8-oxo-7,8-dihydroguanine damage and mitochondrial dysfunction. Analysis of somatic mutations reveals a dose-dependent increase of C:G>A:T substitutions in irradiated samples with mutagenic patterns similar to mutational signatures previously attributed to reactive oxygen species. In summary, this study demonstrates that radiation emitted by UV-nail polish dryers can both damage DNA and permanently engrave mutations on the genomes of primary mouse embryonic fibroblasts, human foreskin fibroblasts, and human epidermal keratinocytes.

Association between acrylamide exposure and sex hormones among premenopausal and postmenopausal women: NHANES, 2013-2016

PURPOSE

Acrylamide (AA) is a potential carcinogen that mainly comes from fried, baked and roasted foods, and Hb adducts of AA (HbAA) and its metabolite glycidamide (HbGA) are the biomarkers of its exposure. Increasing evidence suggests that AA is associated with various hormone-related cancers. This study aims to explore the association of HbAA and HbGA with female serum sex hormone concentrations.

METHODS

942 women from the National Health and Nutrition Examination Survey cycles (2013-2016) were included in this cross-sectional study. The associations between HbAA or HbGA or HbGA/HbAA and sex hormones were assessed by the multiple linear regression. Further stratified analyses were conducted to figure out the effects of menopausal status, BMI and smoking status on sex hormone levels.

RESULTS

Among all participants, 597 were premenopausal and 345 were postmenopausal. HbAA was positively associated with both two androgen indicators. Specifically, a ln-unit increase in HbAA was associated with 0.41 ng/dL higher ln(total testosterone, TT) (95% CI 0.00, 0.27) and 0.14 ng/dL higher ln(free testosterone) (95%CI 0.00, 0.28), respectively. However, HbGA concentrations had no association with sex hormones in the overall population. Additionally, HbGA/HbAA was negatively associated with TT and SHBG in the overall population as well as postmenopausal women. In stratified analysis, higher HbAA was associated with rising TT in postmenopausal women (β = 0.29, 95%CI 0.04, 0.53) and underweight/normal-weight women (β = 0.18, 95%CI 0.03, 0.33). Other indicators had no significant association detected in estradiol and sex hormone-binding globulin.

CONCLUSION

Our results revealed that HbAA was positively associated with androgen concentrations, especially in postmenopausal and BMI < 25 women.

Machine learning prediction of exposure to acrylamide based on modelling of association between dietary exposure and internal biomarkers

The ubiquitous occurrence of acrylamide in various thermal processing food products poses a potential health risk for the public. An accurate exposure assessment is crucial to the risk evaluation of acrylamide. Machine learning emerging as a powerful computational tool for prediction was employed to establish the association between internal exposure and dietary exposure to acrylamide among a Chinese cohort of middle-aged and elderly population (n = 1,272). Five machine learning regression models were constructed and compared to predict the daily dietary acrylamide exposure based on urinary biomarkers including N-acetyl-S-(2-carbamoylethyl)-L-cysteine (AAMA), N-acetyl-S-(2-carbamoylethyl)-L-cysteine-sulfoxide (AAMA-sul), N-acetyl-S-(2-carbamoyl-2-hydroxyethyl)-L-cysteine (GAMA), and N-acetyl-S-(1-carbamoyl-2-hydroxyethyl)-L-cysteine (iso-GAMA). Other important covariates such as age, gender, physical activities, and total energy intake were also considered as predictors in the models. Average dietary intake of acrylamide among Chinese elderly participants was 8.9 μg/day, while average urinary contents of AAMA, AAMA-sul, GAMA, and iso-GAMA were 52.2, 19.1, 4.4, and 1.7 nmol/g Ucr (urine creatinine), respectively. Support vector regression (SVR) model showed the best prediction performance with a R of 0.415, followed by light gradient boosting machine (LightGBM) model (R = 0.396), adjusted multiple linear regression (MLR) model (R = 0.378), neural networks (NN) model (R = 0.365), MLR model (R = 0.363), and extreme gradient boosting (XGBoost) model (R = 0.337). The present study firstly correlated dietary exposure with internal exposure to acrylamide among Chinese elderly population, providing an innovative perspective for the exposure assessment of acrylamide.

Aristolochic acid-associated cancers: a public health risk in need of global action

Aristolochic acids (AAs) are a group of naturally occurring compounds present in many plant species of the Aristolochiaceae family. Exposure to AA is a significant risk factor for severe nephropathy, and urological and hepatobiliary cancers (among others) that are often recurrent and characterized by the prominent mutational fingerprint of AA. However, herbal medicinal products that contain AA continue to be manufactured and marketed worldwide with inadequate regulation, and possible environmental exposure routes receive little attention. As the trade of food and dietary supplements becomes increasingly globalized, we propose that further inaction on curtailing AA exposure will have far-reaching negative effects on the disease trends of AA-associated cancers. Our Review aims to systematically present the historical and current evidence for the mutagenicity and carcinogenicity of AA, and the effect of removing sources of AA exposure on cancer incidence trends. We discuss the persisting challenges of assessing the scale of AA-related carcinogenicity, and the obstacles that must be overcome in curbing AA exposure and preventing associated cancers. Overall, this Review aims to strengthen the case for the implementation of prevention measures against AA's multifaceted, detrimental and potentially fully preventable effects on human cancer development.

Dietary Acrylamide Exposure and Risk of Site-Specific Cancer: A Systematic Review and Dose-Response Meta-Analysis of Epidemiological Studies

Diet is a main source of acrylamide exposure to humans. Existing observational data on the relationship between dietary exposure to acrylamide and risk of cancer are inconsistent. We performed a systematic review and dose-response meta-analysis of epidemiological studies evaluating the association between dietary acrylamide exposure and several site-specific cancer. A systematic literature search was conducted in PubMed, Scopus, and Web of Science databases until March 7, 2022. Studies were eligible if they were carried out in non-occupationally exposed adults, assessed dietary acrylamide exposure (μg/day) and reported risk estimates of cancer incidence (all but gynecological cancers). Using a random-effects model, we performed a meta-analysis of site-specific cancer risk comparing the highest vs. lowest category of dietary acrylamide exposure. We also carried out a one-stage dose-response meta-analysis assessing the shape of the association. Out of 1,994 papers screened, 31 were eligible (total of 16 studies), which included 1,151,189 participants in total, out of whom 48,175 developed cancer during the median follow-up period of 14.9 years (range 7.3–33.9). The mean estimated dose of dietary acrylamide across studies was 23 μg/day. Pooled analysis showed no association between the highest vs. lowest dietary acrylamide exposure and each site-specific cancer investigated, with no evidence of thresholds in the dose-response meta-analysis. There were also no associations between dietary acrylamide exposure and the risk of cancers when stratifying by smoking status, except for increased risk of lung cancer in smokers. In conclusion, high dietary acrylamide exposure was not associated with an increased risk of site-specific non-gynecological cancer.

Acrylamide in widely consumed foods - a review

Acrylamide (AA) is considered genotoxic, neurotoxic and a 'probable human carcinogen'. It is included in group 2 A of the International Agency for Research on Cancer (IARC). The formation of AA occurs when starch-based foods are subjected to temperatures higher than 120 °C in an atmosphere with very low water content. The aim of this review is to shed light on the toxicological aspects of AA, showing its regulatory evolution, and describing the most interesting mitigation techniques for each food category involved, with a focus on compliance with EU legislation in the various classes of consumer products of industrial origin in Europe.

Assessment of the genotoxicity of acrylamide

EFSA was requested to deliver a statement on a recent publication revisiting the evidence for genotoxicity of acrylamide (AA). The statement was prepared by a Working Group and was endorsed by the CONTAM Panel before its final approval. In interpreting the Terms of Reference, the statement considered the modes of action underlying the carcinogenicity of AA including genotoxic and non‐genotoxic effects. Relevant publications since the 2015 CONTAM Panel Opinion on AA in food were reviewed. Several new studies reported positive results on the clastogenic and mutagenic properties of AA and its active metabolite glycidamide (GA). DNA adducts of GA were induced by AA exposure in experimental animals and have also been observed in humans. In addition to the genotoxicity of AA, there is evidence for both secondary DNA oxidation via generation of reactive oxygen species and for non‐genotoxic effects which may contribute to carcinogenesis by AA. These studies extend the information assessed by the CONTAM Panel in its 2015 Opinion, and support its conclusions. That Opinion applied the margin of exposure (MOE) approach, as recommended in the EFSA Guidance for substances that are both genotoxic and carcinogenic, for risk characterisation of the neoplastic effects of AA. Based on the new data evaluated, the MOE approach is still considered appropriate, and an update of the 2015 Opinion is not required at the present time.

Analgesic Opioid Ligand Discovery Based on Nonmorphinan Scaffolds Derived from Natural Sources

Strong opioid analgesics, including morphine, are the mainstays for treating moderate to severe acute pain and alleviating chronic cancer pain. However, opioid-related adverse effects, including nausea or vomiting, sedation, respiratory depression, constipation, pruritus (itch), analgesic tolerance, and addiction and abuse liability, are problematic. In addition, the use of opioids to relieve chronic noncancer pain is controversial due to the "opioid crisis" characterized by opioid misuse or abuse and escalating unintentional death rates due to respiratory depression. Hence, considerable research internationally has been aimed at the "Holy Grail" of the opioid analgesic field, namely the discovery of novel and safer opioid analgesics with improved opioid-related adverse effects. In this Perspective, medicinal chemistry strategies are addressed, where structurally diverse nonmorphinan-based opioid ligands derived from natural sources were deployed as lead molecules. The current state of play, clinical or experimental status, and novel opioid ligand discovery approaches are elaborated in the context of retaining analgesia with improved safety and reduced adverse effects, especially addiction liability.

Mechanism of reactive oxygen species generation and oxidative DNA damage induced by acrylohydroxamic acid, a putative metabolite of acrylamide

Acrylamide is formed during the heating of food and is also found in cigarette smoke. It is classified by the International Agency for Research on Cancer as a probable human carcinogen (Group 2A). Glycidamide, an epoxide metabolite of acrylamide, is implicated in the mechanism of acrylamide carcinogenicity. Acrylamide causes oxidative DNA damage in target organs. We sought to clarify the mechanism of acrylamide-induced oxidative DNA damage by investigating site-specific DNA damage and reactive oxygen species (ROS) generation by a putative metabolite of acrylamide, acrylohydroxamic acid (AA). Our results, using ³²P-5'-end-labeled DNA fragments, indicated that, although AA alone did not damage DNA, AA treated with amidase induced DNA damage in the presence of Cu(II). DNA cleavage occurred preferentially at T and C, and particularly at T in 5'-TG-3' sequences, and the DNA cleavage pattern was similar to that of hydroxylamine. The DNA damage was inhibited by methional, catalase, and Cu(I)-chelator bathocuproine, suggesting that H₂O₂ and Cu(I) are involved in the mechanism of DNA damage induced by AA treated with amidase. In addition, amidase-treated AA increased 8-oxo-7,8-dihydro-2'-deoxyguanosine formation in calf thymus DNA, an indicator of oxidative DNA damage, in a dose-dependent manner. In conclusion, hydroxylamine, possibly produced from AA treated with amidase, was autoxidized via the Cu(II)/Cu(I) redox cycle and H₂O₂ generation, suggesting that oxidative DNA damage induced by ROS plays an important role in acrylamide-related carcinogenesis.

Association of acrylamide hemoglobin biomarkers with chronic obstructive pulmonary disease in the general population in the US: NHANES 2013-2016

Background: Acrylamide is a well-known potential carcinogenic compound formed as an intermediate in the Maillard reaction during heat treatment, mainly from high-temperature frying, and is found in baked goods and coffee, as well as resulting from water treatment, textiles and paper processing. The effects of acrylamide on lung disease in humans remains unclear. We aimed to investigate the association between blood acrylamide and glycidamide and chronic obstructive pulmonary disease (COPD) in the United States of America (U.S.) population using PROC logistic regression models. Results: 2744 participants aged 20 to 80 from the 2013-2016 National Health and Nutrition Examination Survey (NHANES) were enrolled. After adjusting for demographic data, health factors and serum cotinine, the ratio of HbGA to HbAA (HbGA/HbAA) significantly increased the risk of COPD (P for trend = 0.022). The odds ratio (OR) with a 95% confidence interval (95% CI) for HbGA/HbAA in the third tile was 2.45 (1.12-5.31), compared with the lowest tile. The restricted cubic spline (RCS) curve showed a positive linear correlation between the log (HbGA/HbAA) and the risk of COPD (P = 0.030). Conclusion: The ratio of glycidamide and acrylamide (HbGA/HbAA) was associated with COPD. This association was more prominent in males, obese individuals, people with a poverty income ratio (PIR) < 1.85 or people who never exercise. However, null associations were observed between HbAA, HbGA and HbAA + HbGA, and COPD.

Establishment of Novel Genotoxicity Assay System Using Murine Normal Epithelial Tissue-Derived Organoids

Short-/middle-term and simple prediction studies for carcinogenesis are needed for the safety assessment of chemical substances. To establish a novel genotoxicity assay with an in vivo mimicking system, we prepared murine colonic/pulmonary organoids from gpt delta mice according to the general procedure using collagenase/dispase and cultured them in a 3D environment. When the organoids were exposed to foodborne carcinogens—2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridine (PhIP) and acrylamide (AA)—in the presence of metabolic activation systems, mutation frequencies (MFs) occurring in the gpt gene dose-dependently increased. Moreover, the mutation spectrum analysis indicated predominant G:C to T:A transversion with PhIP, and A:T to C:G and A:T to T:A transversion with AA. These data correspond to those of a previous study describing in vivo mutagenicity in gpt delta mice. However, organoids derived from the liver, a non-target tissue of PhIP-carcinogenesis, also demonstrated genotoxicity with a potency comparable to colonic organoids. Organoids and PhIP were directly incubated in the presence of metabolic activation systems; therefore, there was a lack of organ specificity, as observed in vivo. Additionally, PhIP-DNA adduct levels were comparable in hepatic and colonic organoids after PhIP exposure. Taken together, the organoids prepared in the present study may be helpful to predict chemical carcinogenesis.

Prioritizing cancer hazard assessments for IARC Monographs using an integrated approach of database fusion and text mining

BACKGROUND

Systematic evaluation of literature data on the cancer hazards of human exposures is an essential process underlying cancer prevention strategies. The scope and volume of evidence for suspected carcinogens can range from very few to thousands of publications, requiring a complex, systematically planned, and critical procedure to nominate, prioritize and evaluate carcinogenic agents. To aid in this process, database fusion, cheminformatics and text mining techniques can be combined into an integrated approach to inform agent prioritization, selection, and grouping.

RESULTS

We have applied these techniques to agents recommended for the IARC Monographs evaluations during 2020-2024. An integration of PubMed filters to cover cancer epidemiology, key characteristics of carcinogens, chemical lists from 34 databases relevant for cancer research, chemical structure grouping and a literature data-based clustering was applied in an innovative approach to 119 agents recommended by an advisory group for future IARC Monographs evaluations. The approach also facilitated a rational grouping of these agents and aids in understanding the volume and complexity of relevant information, as well as important gaps in coverage of the available studies on cancer etiology and carcinogenesis.

CONCLUSION

A new data-science approach has been applied to diverse agents recommended for cancer hazard assessments, and its applications for the IARC Monographs are demonstrated. The prioritization approach has been made available at www.cancer.idsl.me site for ranking cancer agents.

Toxic effects of subacute exposure to acrylamide on motor endplates of the gastrocnemius in rats

Acrylamide (ACR) is a recognized toxin that is known to induce neurotoxicity in humans and experimental animals. This study aimed to investigate the toxic effects of subacute exposure of the motor endplate (MEP) of the gastrocnemius in rats to ACR. All rats were randomly divided into control, 9, 18, and 36 mg/kg ACR groups, and ACR was administered by gastric gavage for 21 days. The behavioral tests were performed weekly. On the 22nd day, the wet weight of the gastrocnemius was measured. The changes in muscle fiber structure, nerve endings, and MEP in the gastrocnemius were examined by hematoxylin-eosin (HE) and gold chloride staining. Acetylcholinesterase (AChE) content in the gastrocnemius was detected by AChE staining. The expression of AChE and calcitonin gene-related peptide was detected by immunohistochemistry and western blot. Rats exposed to ACR showed a significant increase in gait scores and hind limb splay distance compared with the control group, and the wet weight of the gastrocnemius was reduced, HE staining showed that the muscle fiber structure of the gastrocnemius became thin and the arrangement was dense with nuclear aggregation, gold chloride staining showed that nerve branches decreased and became thin, nerve fibers became short and light, the number of MEPs was decreased, the staining became light, and the structure was not clear. AChE staining showed that the number of MEPs was significantly reduced after exposure to ACR, the shape became small, and the AChE content decreased in a dose-dependent manner. Immunohistochemistry and western blot analysis results of the expression levels of AChE and CGRP showed a decreasing trend as compared to the control group with increasing ACR exposure dose. The reduction in protein levels may be the mechanism by which ACR has a toxic effect on the MEP in the gastrocnemius of rats.

Geospatial Assessments of DNA Adducts in the Human Stomach: A Model of Field Cancerization

BACKGROUND

Field cancerization is a popular concept regarding where cancer cells arise in a plane, such as the opened-up gastrointestinal mucosa. The geospatial distribution of DNA adducts, some of which are believed to initiate mutation, may be a clue to understanding the landscape of the preferred occurrence of gastric cancer in the human stomach, such that the occurrence is much more frequent in the lesser curvature than in the greater curvature.

METHODS

Seven DNA adducts, C5-methyl-2'-deoxycytidine, 2'-deoxyinosine, C5-hydroxymethyl-2'-deoxycytidine, N6-methyl-2'-deoxyadenosine, 1,N6-etheno-2'-deoxyadenosine, N6-hydroxymethyl-2'-deoxyadenosine, and C8-oxo-2'-deoxyguanosine, from different points and zones of the human stomach were semi quantitatively measured by liquid chromatography/tandem mass spectrometry. The differences in the quantity of these DNA adducts from the lesser and greater curvature, the upper, middle and lower third zones, the anterior and posterior wall of the stomach, and the mucosae distant from and near the tumor were compared to determine whether the location preference of cancer in the stomach could be explained by the distribution of these DNA adducts. Comparisons were conducted considering the tumor locations and operation methods.

CONCLUSIONS

Regarding the DNA adducts investigated, significant differences in quantities and locations in the whole stomach were not noted; thus, these DNA adducts do not explain the preferential occurrence of cancer in particular locations of the human stomach.

Metabolomics analysis of the effects of quercetin on hepatotoxicity induced by acrylamide exposure in rats

Acrylamide (AA) widely exists in human diet, which makes the public inevitably exposed to AA in daily life. Thisstudy aimed to investigatethe effects of quercetin on AA-induced hepatotoxicity utilizing metabolomics technology. Sixty male Wistar Rats were randomly divided into six groups: control, two dosages of quercetinintervention[10 and 50 mg/kgbody weight (bw)], AA-treated [5 mg/kgbw], and two dosages of quercetin combined with AA intervention. AA and quercetin were given to rats via drinking water and gavage respectively. After 16 weeksoftreatment, liver samples were collected for metabolomics analysis. 16metabolites were finally identified, the intensities of glutathione and NADP were decreased (p < 0.01), whereas the intensities of taurodeoxycholic acid, glycocholic acid, cholic acid, sphingosine, sphingosine1-phosphate, stearidonyl carnitine, N-undecanoylglycine, cholesterol, 13,14-Dihydro-15-keto-PGE2, LysoPE (20:5), LysoPE (18:3), LysoPC (20:4), and PC (22:5) were increased (p < 0.01) in the AA-treated groupthan those in the control group. After high-dose quercetin (50 mg/kgbw) plus AA treated concurrently to rats, the contents of the above 16 metabolites were significantly restored. This research showed that 50 mg/kg quercetin can alleviate AA-induced hepatotoxicity by reducing oxidative stress and inflammatory injury and regulating lipid metabolism.

Reduced free asparagine in wheat grain resulting from a natural deletion of TaASN-B2: investigating and exploiting diversity in the asparagine synthetase gene family to improve wheat quality

BACKGROUND

Understanding the determinants of free asparagine concentration in wheat grain is necessary to reduce levels of the processing contaminant acrylamide in baked and toasted wheat products. Although crop management strategies can help reduce asparagine concentrations, breeders have limited options to select for genetic variation underlying this trait. Asparagine synthetase enzymes catalyse a critical step in asparagine biosynthesis in plants and, in wheat, are encoded by five homeologous gene triads that exhibit distinct expression profiles. Within this family, TaASN2 genes are highly expressed during grain development but TaASN-B2 is absent in some varieties.

RESULTS

Natural genetic diversity in the asparagine synthetase gene family was assessed in different wheat varieties revealing instances of presence/absence variation and other polymorphisms, including some predicted to affect the function of the encoded protein. The presence and absence of TaASN-B2 was determined across a range of UK and global common wheat varieties and related species, showing that the deletion encompassing this gene was already present in some wild emmer wheat genotypes. Expression profiling confirmed that TaASN2 transcripts were only detectable in the grain, while TaASN3.1 genes were highly expressed during the early stages of grain development. TaASN-A2 was the most highly expressed TaASN2 homeologue in most assayed wheat varieties. TaASN-B2 and TaASN-D2 were expressed at similar, lower levels in varieties possessing TaASN-B2. Expression of TaASN-A2 and TaASN-D2 did not increase to compensate for the absence of TaASN-B2, so total TaASN2 expression was lower in varieties lacking TaASN-B2. Consequently, free asparagine concentrations in field-produced grain were, on average, lower in varieties lacking TaASN-B2, although the effect was lost when free asparagine accumulated to very high concentrations as a result of sulphur deficiency.

CONCLUSIONS

Selecting wheat genotypes lacking the TaASN-B2 gene may be a simple and rapid way for breeders to reduce free asparagine concentrations in commercial wheat grain.

Progress on reducing acrylamide levels in potato crisps in Europe, 2002 to 2019

European Snacks Association (ESA) data on acrylamide in potato crisps from 2002 to 2019 (99704 observations) were analysed. Acrylamide levels have plateaued since 2011, although the lowest mean so far was attained in 2018 at 353 ± 2.7 ng g^-1: a 54% reduction since 2002. The 85^th, 90^th and 95^th quantiles did show evidence of continued downward progress, the 90^th quantile being lower than the 750 ng g^-1 European Benchmark Level from 2017 to 2019. A smaller dataset from the European Food Safety Authority (2124 observations) for 2011-2018 was also analysed. The yearly means were higher than those of the ESA data but showed a fall in average acrylamide from 715 ± 40.5 ng g^-1 in 2015 to 505 ± 28.5 ng g^-1 in 2018, as well as steep falls in the 85^th, 90^th and 95^th quantiles. Nevertheless, even the 85^th quantile remained above the 750 ng g^-1 Benchmark Level. The ESA data showed a reduction in the proportion of samples with acrylamide exceeding 750 ng g^-1, from over 40% in 2002 to 7.75% in 2019. Seasonality was evident, with highest acrylamide levels from November to May. Crisp type had little effect except that thicker types had a higher proportion of samples containing >750 ng g^-1 acrylamide. Analysis of the region of origin in Europe of the final product revealed improvements in the east and north. Geographical factors combined with seasonality continued to be problematic but was also an aspect in which progress was most evident. The findings show that improvements have been made in reducing the number of samples with very high levels of acrylamide, but do not suggest that mean acrylamide levels could be reduced substantially below where they have been since 2011, or that levels could be kept consistently below the current Benchmark Level.

Effect of sampling time on somatic and germ cell mutations induced by acrylamide in gpt delta mice

Background

Acrylamide (AA) is a rodent carcinogen and classified by the IARC into Group 2A (probable human carcinogen). AA has been reported to induce mutations in transgenic rodent gene mutation assays (TGR assays), the extent of which is presumed to depend on exposure length and the duration of expression after exposure. In particular, it is not clear in germ cells. To investigate mutagenicity with AA in somatic and germ cells at different sampling times, we conducted TGR assays using gpt delta transgenic mice.

Results

The male gpt delta mice at 8 weeks of age were treated with AA at 7.5, 15 and 30 mg/kg/day by gavage for 28 days. Peripheral blood was sampled on the last day of the treatment for micronucleus tests and tissues were sampled for gene mutation assays at day 31 and day 77, those being 3 and 49 days after the final treatment (28 + 3d and 28 + 49d), respectively. Another group of mice was treated with N-Ethyl-N-nitrosourea (ENU) at 50 mg/kg/day by intraperitoneal administration for 5 consecutive days and tissues were sampled at the day 31 and day 77 (5 + 26d and 5 + 72d). Frequencies of micronucleated erythrocytes in the peripheral blood significantly increased at AA doses of 15 and 30 mg/kg/day. Two- to three-fold increases in gpt mutation frequencies (MFs) compared to vehicle control were observed in the testes and lung treated with 30 mg/kg/day of AA at both sampling time. In the sperm, the gpt MFs and G:C to T:A transversions were significantly increased at 28 + 3d, but not at 28 + 49d. ENU induced gpt mutations in these tissues were examined at both 5 + 26d and 5 + 72d. A higher mutant frequency in the ENU-treated sperm was observed at 5 + 72d than that at 5 + 26d.

Conclusions

The gpt MFs in the testes, sperm and lung of the AA-treated mice were determined and compared between different sampling times (3 days or 49 days following 28 day-treatment). These results suggest that spermatogonial stem cells are less sensitive to AA mutagenicity under the experimental condition. Prolonged expression time after exposure to AA to detect mutagenicity may be effective in somatic cells but not in germ cells.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41021-021-00175-5.

Mutagenicity of 2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-OH-PhIP) in human TP53 knock-in (Hupki) mouse embryo fibroblasts

2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a possible human carcinogen formed in cooked fish and meat. PhIP is bioactivated by cytochrome P450 enzymes to form 2-hydroxyamino-1-methyl-6-phenylimidazo[4,5-b]pyridine (N-OH-PhIP), a genotoxic metabolite that reacts with DNA leading to the mutation-prone DNA adduct N-(deoxyguanosin-8-yl)-PhIP (dG-C8-PhIP). Here, we studied N-OH-PhIP-induced whole genome mutagenesis in human TP53 knock-in (Hupki) mouse embryo fibroblasts (HUFs) immortalised and subjected to whole genome sequencing (WGS). In addition, mutagenicity of N-OH-PhIP in TP53 and the lacZ reporter gene were assessed. TP53 mutant frequency in HUF cultures treated with N-OH-PhIP (2.5 μM for 24 h, n = 90) was 10% while no TP53 mutations were found in untreated controls (DMSO for 24 h, n = 6). All N-OH-PhIP-induced TP53 mutations occurred at G:C base pairs with G > T/C > A transversions accounting for 58% of them. TP53 mutations characteristic of those induced by N-OH-PhIP have been found in human tumours including breast and colorectal, which are cancer types that have been associated with PhIP exposure. LacZ mutant frequency increased 25-fold at 5 μM N-OH-PHIP and up to ~350 dG-C8-PhIP adducts/10⁸ nucleosides were detected by ultra-performance liquid chromatography-electrospray ionisation multistage scan mass spectrometry (UPLC-ESI-MS³) at this concentration. In addition, a WGS mutational signature defined by G > T/C > A transversions was present in N-OH-PhIP-treated immortalised clones, which showed similarity to COSMIC SBS4, 18 and 29 signatures found in human tumours.

Asparagine accumulation in chicory storage roots is controlled by translocation and feedback regulation of asparagine biosynthesis in leaves

The presence of acrylamide (AA), a potentially carcinogenic and neurotoxic compound, in food has become a major concern for public health. AA in plant-derived food mainly arises from the reaction of the amino acid asparagine (Asn) and reducing sugars during processing of foodstuffs at high temperature. Using a selection of genotypes from the chicory (Cichorium intybus L.) germplasm, we performed Asn measurements in storage roots and leaves to identify genotypes contrasting for Asn accumulation. We combined molecular analysis and grafting experiments to show that leaf to root translocation controls Asn biosynthesis and accumulation in chicory storage roots. We could demonstrate that Asn accumulation in storage roots depends on Asn biosynthesis and transport from the leaf, and that a negative feedback loop by Asn on CiASN1 expression impacts Asn biosynthesis in leaves. Our results provide a new model for Asn biosynthesis in root crop species and highlight the importance of characterizing and manipulating Asn transport to reduce AA content in processed plant-based foodstuffs.

Mutagenicity of acrylamide and glycidamide in human TP53 knock-in (Hupki) mouse embryo fibroblasts

Acrylamide is a suspected human carcinogen formed during high-temperature cooking of starch-rich foods. It is metabolised by cytochrome P450 2E1 to its reactive metabolite glycidamide, which forms pre-mutagenic DNA adducts. Using the human TP53 knock-in (Hupki) mouse embryo fibroblasts (HUFs) immortalisation assay (HIMA), acrylamide- and glycidamide-induced mutagenesis was studied in the tumour suppressor gene TP53. Selected immortalised HUF clones were also subjected to next-generation sequencing to determine mutations across the whole genome. The TP53-mutant frequency after glycidamide exposure (1.1 mM for 24 h, n = 198) was 9% compared with 0% in cultures treated with acrylamide [1.5 (n = 24) or 3 mM (n = 6) for 48 h] and untreated vehicle (water) controls (n = 36). Most glycidamide-induced mutations occurred at adenines with A > T/T > A and A > G/T > C mutations being the most common types. Mutations induced by glycidamide occurred at specific TP53 codons that have also been found to be mutated in human tumours (i.e., breast, ovary, colorectal, and lung) previously associated with acrylamide exposure. The spectrum of TP53 mutations was further reflected by the mutations detected by whole-genome sequencing (WGS) and a distinct WGS mutational signature was found in HUF clones treated with glycidamide that was again characterised by A > G/T > C and A > T/T > A mutations. The WGS mutational signature showed similarities with COSMIC mutational signatures SBS3 and 25 previously found in human tumours (e.g., breast and ovary), while the adenine component was similar to COSMIC SBS4 found mostly in smokers’ lung cancer. In contrast, in acrylamide-treated HUF clones, only culture-related background WGS mutational signatures were observed. In summary, the results of the present study suggest that glycidamide may be involved in the development of breast, ovarian, and lung cancer.

Revisiting the evidence for genotoxicity of acrylamide (AA), key to risk assessment of dietary AA exposure

The weight of evidence pro/contra classifying the process-related food contaminant (PRC) acrylamide (AA) as a genotoxic carcinogen is reviewed. Current dietary AA exposure estimates reflect margins of exposure (MOEs) < 500. Several arguments support the view that AA may not act as a genotoxic carcinogen, especially not at consumer-relevant exposure levels: Biotransformation of AA into genotoxic glycidamide (GA) in primary rat hepatocytes is markedly slower than detoxifying coupling to glutathione (GS). Repeated feeding of rats with AA containing foods, bringing about uptake of 100 µg/kg/day of AA, resulted in dose x time-related buildup of AA-hemoglobin (Hb) adducts, whereas GA-Hb adducts remained within the background. Since hepatic oxidative biotransformation of AA into GA was proven by simultaneous urinary mercapturic acid monitoring it can be concluded that at this nutritional intake level any GA formed in the liver from AA is quantitatively coupled to GS to be excreted as mercapturic acid in urine. In an oral single dose–response study in rats, AA induced DNA N⁷-GA-Gua adducts dose-dependently in the high dose range (> 100 µg/kg b w). At variance, in the dose range below 100 µg/kg b.w. down to levels of average consumers exposure, DNA N⁷ -Gua lesions were found only sporadically, without dose dependence, and at levels close to the lower bound of similar human background DNA N⁷-Gua lesions. No DNA damage was detected by the comet assay within this low dose range. GA is a very weak mutagen, known to predominantly induce DNA N⁷-GA-Gua adducts, especially in the lower dose range. There is consensus that DNA N⁷-GA-Gua adducts exhibit rather low mutagenic potency. The low mutagenic potential of GA has further been evidenced by comparison to preactivated forms of other process-related contaminants, such as N-Nitroso compounds or polycyclic aromatic hydrocarbons, potent food borne mutagens/carcinogens. Toxicogenomic studies provide no evidence supporting a genotoxic mode of action (MOA), rather indicate effects on calcium signalling and cytoskeletal functions in rodent target organs. Rodent carcinogenicity studies show induction of strain- and species-specific neoplasms, with MOAs not considered likely predictive for human cancer risk. In summary, the overall evidence clearly argues for a nongenotoxic/nonmutagenic MOA underlying the neoplastic effects of AA in rodents. In consequence, a tolerable intake level (TDI) may be defined, guided by mechanistic elucidation of key adverse effects and supported by biomarker-based dosimetry in experimental systems and humans.

Interaction of Acrylamide, Acrolein, and 5-Hydroxymethylfurfural with Amino Acids and DNA

Acrylamide, acrolein, and 5-hydroxymethylfurfural (HMF) are food-borne toxicants produced during the thermal processing of food. The α,β-unsaturated carbonyl group or aldehyde group in their structure can react easily with the amino, imino, and thiol groups in amino acids, proteins, and DNA via Michael addition and nucleophilic reactions in food and in vivo. This work reviews the interaction pathways of three toxins with amino acids and the cytotoxicity and changes after the digestion and absorption of the resulting adducts. Their interaction with DNA is also discussed. Amino acids ubiquitously exist in foods and are added as nutrients or used to control these food-borne toxicants. Hence, the interaction widely occurring in foods would greatly increase the internal exposure of these toxins and their derived compounds after food intake. This review aims to encourage further investigation on toxin-derived compounds, including their types, exposure levels, toxicities, and pharmacokinetics.

Experimental investigations of carcinogen-induced mutation spectra: Innovation, challenges and future directions

Recent years have witnessed an expansion of mutagenesis research focusing on experimentally modeled genome-scale mutational signatures of carcinogens and of endogenous processes. Experimental mutational signatures can explain etiologic links to patterns found in human tumors that may be linked to same exposures, and can serve as biomarkers of exposure history and may even provide insights on causality. A number of innovative exposure models have been employed and reported, based on cells cultured in monolayers or in 3-D, on organoids, induced pluripotent stem cells, non-mammalian organisms, microorganisms and rodent bioassays. Here we discuss some of the latest developments and pros and cons of these experimental systems used in mutational signature analysis. Integrative designs that bring together multiple exposure systems (in vitro, in vivo and in silico pan-cancer data mining) started emerging as powerful tools to identify robust mutational signatures of the tested cancer risk agents. We further propose that devising a new generation of cell-based models is warranted to streamline systematic testing of carcinogen effects on the cell genomes, while seeking to increasingly supplant animal with non-animal systems to address relevant ethical issues and accentuate the 3R principles. We conclude that the knowledge accumulating from the growing body of signature modelling investigations has considerable power to advance cancer etiology studies and to support cancer prevention efforts through streamlined characterization of cancer-causing agents and the recognition of their specific effects.

Kampani D, Al Hasham N, M. Assker M, Shawa N, Saleh D, Alfarouk KO. Assessing the Knowledge of Environmental Risk Factors for Cancer among the UAE Population: A Pilot Study

The incidence of cancer is increasing worldwide as well as in the United Arab Emirates (UAE). Currently, researchers are advocating not only for prevention programs but also for early detection. In this study, we aimed to assess the general awareness of cancer among the UAE population, with a focus on environmental risk factors. A descriptive cross-sectional design was employed, and a structured questionnaire was used to collect data from 385 participants. A total of 91.2% of the study population identified cancer as the leading cause of death, while 64.6% of the subjects were able to identify the key causes of cancer. A total of 87.3% and 70.5% of the participants were able to define tobacco and alcohol, respectively, as cancer-causing agents. Most of the study population failed to identify cancer-related infectious agents and incense smoke as carcinogens. Respondents in the medical professions had the highest knowledge score when compared with respondents with a non-medical profession and unemployed participants (p < 0.0005). To fill the gaps in cancer-related knowledge, participants were asked about their preferred method for cancer education, and 83.9% of the participants favored the media as a source of information. Conclusively, our findings indicated a gap in cancer knowledge among UAE residents, which highlights the importance of educational campaigns by health authorities; a follow-up study evaluating the success of educational campaigns is also warranted.

The promise of toxicogenomics for genetic toxicology: past, present and future

Toxicogenomics, the application of genomics to toxicology, was described as 'a new era' for toxicology. Standard toxicity tests typically involve a number of short-term bioassays that are costly, time consuming, require large numbers of animals and generally focus on a single end point. Toxicogenomics was heralded as a way to improve the efficiency of toxicity testing by assessing gene regulation across the genome, allowing rapid classification of compounds based on characteristic expression profiles. Gene expression microarrays could measure and characterise genome-wide gene expression changes in a single study and while transcriptomic profiles that can discriminate between genotoxic and non-genotoxic carcinogens have been identified, challenges with the approach limited its application. As such, toxicogenomics did not transform the field of genetic toxicology in the way it was predicted. More recently, next generation sequencing (NGS) technologies have revolutionised genomics owing to the fact that hundreds of billions of base pairs can be sequenced simultaneously cheaper and quicker than traditional Sanger methods. In relation to genetic toxicology, and thousands of cancer genomes have been sequenced with single-base substitution mutational signatures identified, and mutation signatures have been identified following treatment of cells with known or suspected environmental carcinogens. RNAseq has been applied to detect transcriptional changes following treatment with genotoxins; modified RNAseq protocols have been developed to identify adducts in the genome and Duplex sequencing is an example of a technique that has recently been developed to accurately detect mutation. Machine learning, including MutationSeq and SomaticSeq, has also been applied to somatic mutation detection and improvements in automation and/or the application of machine learning algorithms may allow high-throughput mutation sequencing in the future. This review will discuss the initial promise of transcriptomics for genetic toxicology, and how the development of NGS technologies and new machine learning algorithms may finally realise that promise.

Coffee drinking and cancer risk: an umbrella review of meta-analyses of observational studies

BACKGROUND

Epidemiological studies on the association between coffee intake and cancer risk have yielded inconsistent results. To summarize and appraise the quality of the current evidence, we conducted an umbrella review of existing findings from meta-analyses of observational studies.

METHODS

We searched PubMed, Embase, Web of Science and the Cochrane database to obtain systematic reviews and meta-analyses of associations between coffee intake and cancer incidence. For each association, we estimated the summary effect size using the fixed- and random-effects model, the 95% confidence interval, and the 95% prediction interval. We also assessed heterogeneity, evidence of small-study effects, and excess significance bias.

RESULTS

Twenty-eight individual meta-analyses including 36 summary associations for 26 cancer sites were retrieved for this umbrella review. A total of 17 meta-analyses were significant at P ≤ 0.05 in the random-effects model. For the highest versus lowest categories, 4 of 26 associations had a more stringent P value (P ≤ 10- 6). Associations for five cancers were significant in dose-response analyses. Most studies (69%) showed low heterogeneity (I2 ≤ 50%). Three and six associations had evidence of excessive significance bias and publication bias, respectively. Coffee intake was inversely related to the risk of liver cancer and endometrial cancer and was characterized by dose-response relationships. There were no substantial changes when we restricted analyses to meta-analysis of cohort studies.

CONCLUSIONS

There is highly suggestive evidence for an inverse association between coffee intake and risk of liver and endometrial cancer. Further research is needed to provide more robust evidence for cancer at other sites.

The repertoire of mutational signatures in human cancer

Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic mutational signature¹. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium² of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we characterized mutational signatures using 84,729,690 somatic mutations from 4,645 whole-genome and 19,184 exome sequences that encompass most types of cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4 clustered-base-substitution and 17 small insertion-and-deletion signatures. The substantial size of our dataset, compared with previous analyses^3-15, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unknown cause. This analysis provides a systematic perspective on the repertoire of mutational processes that contribute to the development of human cancer.

Strategies and Challenges for the Development of Industrial Enzymes Using Fungal Cell Factories

Industrial enzymes have been produced from microorganisms for more than a century. Today, a large share of enzyme products is manufactured using recombinant microorganisms. This chapter focuses on major industrial fungal species belonging to the ascomycetes like Aspergillus niger, A. oryzae, and Trichoderma reesei. Many of the commercially available recombinant enzymes are manufactured using fungi. Examples of fungal enzymes used in food products are described. The enzyme industry is to a large extent cost-driven, so the enzyme product needs to meet strict COGS (cost of goods sold) targets. Therefore, the cell factory must be very efficient to produce the enzyme in high titers and efficiently utilize raw materials. Secondly, it must be designed for a robust and generic fermentation process. When developing fungal hosts for enzyme production, several properties of the system need to be considered relating to efficiency of the cell factory, purity of the product, and safety of both the cell factory and the product. Purity is secured by engineering of the cell factory, and properties related to safety must also be engineered into the fungal host. The methods used for strain improvement are continuously being developed to increase yields and are described herein. More automation using precision tools for modification of the genome (i.e., CRISPR) and low-cost sequencing have vastly expanded the possibilities and enabled fast strain development. Using systems biology approaches, better understanding of cellular processes is now possible enabling advanced engineering of fungal cell factories. Surprisingly, a survey of innovation in the field revealed a decrease in the number of patent applications in recent years. Finally, the requirements for enzyme approval, especially in food and feed, have increased significantly worldwide in the last few years. A description of the regulatory landscape and its challenges in food and feed is included.

Characterising Mutational Spectra of Carcinogens in the Tumour Suppressor Gene TP53 Using Human TP53 Knock-in (Hupki) Mouse Embryo Fibroblasts

DNA in dividing cells is prone to mutagenesis, with mutations making key contributions to human disease including cancer. The tumour suppressor gene TP53 is the most frequently mutated gene in human tumours. Here, we present a robust protocol for studying TP53 mutagenesis utilising human TP53 knock-in (Hupki) mouse embryonic fibroblasts (HUFs). In the HUF immortalisation assay (HIMA), primary HUFs are treated with known or suspected carcinogens at 3% oxygen and then transferred to 20% atmospheric oxygen to induce senescence. Cells containing mutations (e.g., in TP53) that allow bypassing of senescence eventually emerge as immortalised clonal cell lines after 2-3 months of serial passaging. As not all immortalised HUF cells contain TP53 mutations, we developed a Nutlin-3a counter-screen to select for TP53-mutated clones prior to sequencing. TP53 mutation spectra generated can be compared with those of human tumours recorded in the International Agency for Research on Cancer TP53 mutation database. Environmental mutagens that have demonstrated and validated the utility of the HIMA include ultraviolet radiation, aristolochic acid, and benzo[a]pyrene. The TP53 mutation patterns induced by these mutagens in the HIMA corresponded to those found in human tumours from patients exposed to these mutagens. The approach presented helps to deepen our understanding of human cancer aetiology.

Acrylamide in food: Progress in and prospects for genetic and agronomic solutions

Acrylamide is a processing contaminant and Group 2a carcinogen that was discovered in foodstuffs in 2002. Its presence in a range of popular foods has become one of the most difficult problems facing the food industry and its supply chain. Wheat, rye and potato products are major sources of dietary acrylamide, with biscuits, breakfast cereals, bread (particularly toasted), crispbread, batter, cakes, pies, French fries, crisps and snack products all affected. Here we briefly review the history of the issue, detection methods, the levels of acrylamide in popular foods and the risk that dietary acrylamide poses to human health. The pathways for acrylamide formation from free (non-protein) asparagine are described, including the role of reducing sugars such as glucose, fructose and maltose and the Maillard reaction. The evolving regulatory situation in the European Union and elsewhere is discussed, noting that food businesses and their suppliers must plan to comply not only with current regulations but with possible future regulatory scenarios. The main focus of the review is on the genetic and agronomic approaches being developed to reduce the acrylamide-forming potential of potatoes and cereals and these are described in detail, including variety selection, plant breeding, biotechnology and crop management. Obvious targets for genetic interventions include asparagine synthetase genes, and the asparagine synthetase gene families of different crop species are compared. Current knowledge on crop management best practice is described, including maintaining optimum storage conditions for potatoes and ensuring sulphur sufficiency and disease control for wheat.

Experimental Delineation of Mutational Signatures Is an Essential Tool in Cancer Epidemiology and Prevention

Advances in experimental modeling of the mutational signatures of environmental exposures and endogenous mutagenic processes will elucidate the role of mutagenesis in cancer, facilitate carcinogen classification, and enable new molecular cancer epidemiology studies.

French infant total diet study: Dietary exposure to heat-induced compounds (acrylamide, furan and polycyclic aromatic hydrocarbons) and associated health risks

A total diet study (TDS) was conducted between 2010 and 2016 to assess the risk associated with chemicals in food of non-breast-fed children from 1 to 36 months living in France. Food samples were collected, prepared "as consumed", and analyzed for chemicals of public health interest. Acrylamide, furan and polycyclic aromatic hydrocarbons (PAHs) were analyzed as heat-induced compounds produced mainly during thermal processing of foods. Dietary exposure was assessed for 705 representative children using food consumptions recorded through a 3-consecutive-days record. As all calculated margins of exposure (MOE) for PAHs exceeded 10 000, dietary exposure of the infant and toddler population was deemed tolerable with regard to the carcinogenic risk. Conversely, the exposure levels to acrylamide and furan were considered as of concern, requiring management measures to reduce the exposure essentially by reducing the formation of heat-induced compounds during food production or preparation processes. Efforts should mainly focus on major contributors to the exposure, i.e. sweet and savoury biscuits and bars, and potatoes and potato products for acrylamide, baby jars of vegetables, with or without meat or fish for acrylamide and furan.